Operating Model: StonesSheep_WMU42
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25 April 2018
Introduction
Completing the OM Documentation
This document is used to generate a HTML OM report document.
The document is separated into 7 sections:
Introduction (this section)
Custom Parameters (optional)
Stock Parameters
Fleet Parameters
Obs (Observation) Parameters
Imp (Implementation) Parameters
References
The Introduction section is used to briefly describe the fishery and the details of the Operating Model.
It should include an explanation for the OM parameters:
nsim: the number of simulations.
proyears: the number of projectio years.
interval: the management interval.
pstar: the percentile of the sample of the management recommendation for each method.
maxF: the maximum instantaneous fishing mortality rate that may be simulated for any given age class.
reps: the number of samples of the management recommendation for each method.
The Custom Parameters section is optional and should only be included if the cpars feature of DLMtool is used in the OM.
Delete both the heading and the text in this section if cpars are not used.
The Stock, Fleet, Obs, and Imp sections include each slot in these components of the OM object.
Provide details (including references where applicable) for the choice of values for each slot below the corresponding slot name (e.g., ## M).
For example:
M
An explanation for the values of the natural mortality rate in the OM (Smith et al. 1999).
You do not need to include the actual values from the OM. These will be included automatically in the final compiled document.
References should be included in the ‘References’ section at the end of the document.
Once complete, this text file will be compiled into an OM Report Document.
This text file is linked to the Excel spreadsheet that was generated with the same file name.
It serves as a single documentation source for a DLMtool OM, and should be updated whenever parameter values in the OM spreadsheet are updated.
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Operating Model
The OM rdata file can be downloaded from here
Download and import into R using myOM <- readRDS('OM.rdata')
OM Parameters
OM Name: Name of the operating model: StonesSheep_WMU42
nsim: The number of simulations: 200
proyears: The number of projected years: 50
interval: The assessment interval - how often would you like to update the management system? 4
pstar: The percentile of the sample of the management recommendation for each method: 0.5
maxF: Maximum instantaneous fishing mortality rate that may be simulated for any given age class: 0.8
reps: Number of samples of the management recommendation for each method. Note that when this is set to 1, the mean value of the data inputs is used. 1
Source: A reference to a website or article from which parameters were taken to define the operating model
SRA and literature review
Stock Parameters
Mortality and age: maxage, R0, M, M2, Mexp, Msd, Mgrad
maxage: The maximum age of individuals that is simulated (there is no plus group ). Single value. Positive integer
Specified Value(s): 16, 16
No justification provided.
R0: The magnitude of unfished recruitment. Single value. Positive real number
Specified Value(s): 294.05, 294.05
No justification provided.
M: Natural mortality rate. Uniform distribution lower and upper bounds. Positive real number
Specified Value(s): 0.53, 0.61
No justification provided.
M2: (Optional) Natural mortality rate at age. Vector of length maxage . Positive real number
Specified Value(s): 0.55, 0.08, 0.04, 0.05, 0.06, 0.07, 0.11, 0.16, 0.27, 0.42, 0.78, 1.21, 1.21, 1.21, 1.21, 1.21
No justification provided.
Mexp: Exponent of the Lorenzen function assuming an inverse relationship between M and weight. Uniform distribution lower and upper bounds. Real numbers <= 0.
Specified Value(s): 0, 0
No justification provided.
Msd: Inter-annual variability in natural mortality rate expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.06, 0.15
No justification provided.
Mgrad: Mean temporal trend in natural mortality rate, expressed as a percentage change in M per year. Uniform distribution lower and upper bounds. Real numbers
Specified Value(s): 0, 0
No justification provided.
Recruitment: h, SRrel, Perr, AC
h: Steepness of the stock recruit relationship. Uniform distribution lower and upper bounds. Values from 1/5 to 1
Specified Value(s): 0.75, 0.9
No justification provided.
SRrel: Type of stock-recruit relationship. Single value, switch (1) Beverton-Holt (2) Ricker. Integer
Specified Value(s): 1, 1
No justification provided.
Perr: Process error, the CV of lognormal recruitment deviations. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.94, 1.06
No justification provided.
AC: Autocorrelation in recruitment deviations rec(t)=ACrec(t-1)+(1-AC)sigma(t). Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.26, 0.63
No justification provided.
Non-stationarity in stock productivity: Period, Amplitude
Period: (Optional) Period for cyclical recruitment pattern in years. Uniform distribution lower and upper bounds. Non-negative real numbers
Slot not used.
Amplitude: (Optional) Amplitude in deviation from long-term average recruitment during recruitment cycle (eg a range from 0 to 1 means recruitment decreases or increases by up to 100% each cycle). Uniform distribution lower and upper bounds. 0 < Amplitude < 1
Slot not used.
Growth: Linf, K, t0, LenCV, Ksd, Kgrad, Linfsd, Linfgrad
Linf: Maximum length. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 100.13, 133.54
No justification provided.
K: von Bertalanffy growth parameter k. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.33, 0.42
No justification provided.
t0: von Bertalanffy theoretical age at length zero. Uniform distribution lower and upper bounds. Non-positive real numbers
Specified Value(s): -0.1, 0.1
No justification provided.
LenCV: Coefficient of variation of length-at-age (assumed constant for all age classes). Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1, 0.12
No justification provided.
Ksd: Inter-annual variability in growth parameter k. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No justification provided.
Kgrad: Mean temporal trend in growth parameter k, expressed as a percentage change in k per year. Uniform distribution lower and upper bounds. Real numbers
Specified Value(s): 0, 0
No justification provided.
Linfsd: Inter-annual variability in maximum length. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No justification provided.
Linfgrad: Mean temporal trend in maximum length, expressed as a percentage change in Linf per year. Uniform distribution lower and upper bounds. Real numbers
Specified Value(s): 0, 0
No justification provided.
Maturity: L50, L50_95
L50: Length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 65.07, 79.2
No justification provided.
L50_95: Length increment from 50 percent to 95 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 10.03, 28.21
No justification provided.
Stock depletion: D
D: Current level of stock depletion SSB(current)/SSB(unfished). Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 0.65, 0.75
No justification provided.
Length-weight conversion parameters: a, b
a: Length-weight parameter alpha. Single value. Positive real number
Specified Value(s): 1, 1
No justification provided.
b: Length-weight parameter beta. Single value. Positive real number
Specified Value(s): 1, 1
No justification provided.
Spatial distribution and movement: Size_area_1, Frac_area_1, Prob_staying
Size_area_1: The size of area 1 relative to area 2. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5, 0.5
No justification provided.
Frac_area_1: The fraction of the unfished biomass in stock 1. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5, 0.5
No justification provided.
Prob_staying: The probability of inviduals in area 1 remaining in area 1 over the course of one year. Uniform distribution lower and upper bounds. Positive fraction.
Specified Value(s): 0.5, 0.5
No justification provided.
Discard Mortality: Fdisc
Fdisc: Fraction of discarded fish that die. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No justification provided.
Fleet Parameters
Historical years of fishing, spatial targeting: nyears, Spat_targ
nyears: The number of years for the historical spool-up simulation. Single value. Positive integer
Specified Value(s): 42
No justification provided.
Spat_targ: Distribution of fishing in relation to spatial biomass: fishing distribution is proportional to B^Spat_targ. Uniform distribution lower and upper bounds. Real numbers
Specified Value(s): 1, 1
No justification provided.
Trend in historical fishing effort (exploitation rate), interannual variability in fishing effort: EffYears, EffLower, EffUpper, Esd
EffYears: Years representing join-points (vertices) of time-varying effort. Vector. Non-negative real numbers
No justification provided.
EffLower: Lower bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
No justification provided.
EffUpper: Upper bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
No justification provided.
| EffYears | EffLower | EffUpper |
|---|---|---|
| 1975 | 0.04 | 0.04 |
| 1976 | 0.02 | 0.02 |
| 1977 | 0.05 | 0.05 |
| 1978 | 0.04 | 0.04 |
| 1979 | 0.05 | 0.05 |
| 1980 | 0.04 | 0.04 |
| 1981 | 0.04 | 0.04 |
| 1982 | 0.03 | 0.03 |
| 1983 | 0.03 | 0.03 |
| 1984 | 0.02 | 0.02 |
| 1985 | 0.03 | 0.03 |
| 1986 | 0.03 | 0.03 |
| 1987 | 0.03 | 0.03 |
| 1988 | 0.04 | 0.04 |
| 1989 | 0.05 | 0.05 |
| 1990 | 0.05 | 0.05 |
| 1991 | 0.05 | 0.05 |
| 1992 | 0.05 | 0.05 |
| 1993 | 0.07 | 0.07 |
| 1994 | 0.05 | 0.05 |
| 1995 | 0.05 | 0.05 |
| 1996 | 0.04 | 0.04 |
| 1997 | 0.05 | 0.05 |
| 1998 | 0.04 | 0.04 |
| 1999 | 0.05 | 0.05 |
| 2000 | 0.04 | 0.04 |
| 2001 | 0.04 | 0.04 |
| 2002 | 0.03 | 0.03 |
| 2003 | 0.03 | 0.03 |
| 2004 | 0.02 | 0.02 |
| 2005 | 0.03 | 0.03 |
| 2006 | 0.03 | 0.03 |
| 2007 | 0.03 | 0.03 |
| 2008 | 0.03 | 0.03 |
| 2009 | 0.02 | 0.02 |
| 2010 | 0.02 | 0.02 |
| 2011 | 0.03 | 0.03 |
| 2012 | 0.04 | 0.04 |
| 2013 | 0.04 | 0.04 |
| 2014 | 0.05 | 0.05 |
| 2015 | 0.04 | 0.04 |
| 2016 | 0.04 | 0.04 |
Esd: Additional inter-annual variability in fishing mortality rate. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No justification provided.
Annual increase in catchability, interannual variability in catchability: qinc, qcv
qinc: Average percentage change in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.03, 1.97
No justification provided.
qcv: Inter-annual variability in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.1, 0.1
No justification provided.
Fishery gear length selectivity: L5, LFS, Vmaxlen, isRel
L5: Shortest length corresponding to 5 percent vulnerability. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 75, 75
No justification provided.
LFS: Shortest length that is fully vulnerable to fishing. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 90, 90
No justification provided.
Vmaxlen: The vulnerability of fish at Stock@Linf. Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 1, 1
No justification provided.
isRel: Selectivity parameters in units of size-of-maturity (or absolute eg cm). Single value. Boolean.
Specified Value(s): 0
No justification provided.
Fishery length retention: LR5, LFR, Rmaxlen, DR
LR5: Shortest length corresponding ot 5 percent retention. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No justification provided.
LFR: Shortest length that is fully retained. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No justification provided.
Rmaxlen: The retention of fish at Stock@Linf. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 1, 1
No justification provided.
DR: Discard rate - the fraction of caught fish that are discarded. Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 0, 0
No justification provided.
Time-varying selectivity: SelYears, AbsSelYears, L5Lower, L5Upper, LFSLower, LFSUpper, VmaxLower, VmaxUpper
SelYears: (Optional) Years representing join-points (vertices) at which historical selectivity pattern changes. Vector. Positive real numbers
Slot not used.
AbsSelYears: (Optional) Calendar years corresponding with SelYears (eg 1951, rather than 1), used for plotting only. Vector (of same length as SelYears). Positive real numbers
Slot not used.
L5Lower: (Optional) Lower bound of L5 (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
L5Upper: (Optional) Upper bound of L5 (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
LFSLower: (Optional) Lower bound of LFS (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
LFSUpper: (Optional) Upper bound of LFS (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
VmaxLower: (Optional) Lower bound of Vmaxlen (use ChooseSelect function to set these). Vector. Fraction
Slot not used.
VmaxUpper: (Optional) Upper bound of Vmaxlen (use ChooseSelect function to set these). Vector. Fraction
Slot not used.
Current Year: CurrentYr
CurrentYr: The current calendar year (final year) of the historical simulations (eg 2011). Single value. Positive integer.
Specified Value(s): 2016
No justification provided.
Existing Spatial Closures: MPA
MPA: (Optional) Matrix specifying spatial closures for historical years. Each row should contain year index (e.g 10 for 10th historical year) followed by fraction of area closed to fishing for each area. i.e. each row represents a change and the number of columns is nareas + 1. The spatial closures are assumed to remain in place for the future projections unless changed by a MP. Default (if left blank) is all areas are open to fishing in historical period.
Slot not used.
Obs Parameters
Catch statistics: Cobs, Cbiascv, CAA_nsamp, CAA_ESS, CAL_nsamp, CAL_ESS
Cobs: Log-normal catch observation error expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.01, 0.02
No justification provided.
Cbiascv: Log-normal coefficient of variation controlling the sampling of bias in catch observations for each simulation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.01
No justification provided.
CAA_nsamp: Number of catch-at-age observation per time step. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 41, 60
No justification provided.
CAA_ESS: Effective sample size (independent age draws) of the multinomial catch-at-age observation error model. Uniform distribution lower and upper bounds. Positive integers
Specified Value(s): 41, 60
No justification provided.
CAL_nsamp: Number of catch-at-length observation per time step. Uniform distribution lower and upper bounds. Positive integers
Specified Value(s): 41, 60
No justification provided.
CAL_ESS: Effective sample size (independent length draws) of the multinomial catch-at-length observation error model. Uniform distribution lower and upper bounds. Positive integers
Specified Value(s): 41, 60
No justification provided.
Index imprecision, bias and hyperstability: Iobs, Ibiascv, Btobs, Btbiascv, beta
Iobs: Observation error in the relative abundance indices expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.05, 0.1
No justification provided.
Ibiascv: Log-normal coefficient of variation controlling error in observations of relative abundance index. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2
No justification provided.
Btobs: Log-normal coefficient of variation controlling error in observations of current stock biomass among years. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.05, 0.1
No justification provided.
Btbiascv: Uniform-log bounds for sampling persistent bias in current stock biomass. Uniform-log distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.02, 0.05
No justification provided.
beta: A parameter controlling hyperstability/hyperdepletion where values below 1 lead to hyperstability (an index that decreases slower than true abundance) and values above 1 lead to hyperdepletion (an index that decreases more rapidly than true abundance). Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 1, 1
No justification provided.
Bias in maturity, natural mortality rate and growth parameters: LenMbiascv, Mbiascv, Kbiascv,t0biascv, Linfbiascv
LenMbiascv: Log-normal coefficient of variation for sampling persistent bias in length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Mbiascv: Log-normal coefficient of variation for sampling persistent bias in observed natural mortality rate. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Kbiascv: Log-normal coefficient of variation for sampling persistent bias in observed growth parameter K. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
t0biascv: Log-normal coefficient of variation for sampling persistent bias in observed t0. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Linfbiascv: Log-normal coefficient of variation for sampling persistent bias in observed maximum length. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Bias in length at first capture, length at full selection: LFCbiascv, LFSbiascv
LFCbiascv: Log-normal coefficient of variation for sampling persistent bias in observed length at first capture. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
LFSbiascv: Log-normal coefficient of variation for sampling persistent bias in length-at-full selection. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Bias in fishery reference points, unfished biomass, FMSY, FMSY/M ratio, biomass at MSY relative to unfished: FMSYbiascv, FMSY_Mbiascv, BMSY_B0biascv
FMSYbiascv: Log-normal coefficient of variation for sampling persistent bias in FMSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.4
No justification provided.
FMSY_Mbiascv: Log-normal coefficient of variation for sampling persistent bias in FMSY/M. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
BMSY_B0biascv: Log-normal coefficient of variation for sampling persistent bias in BMSY relative to unfished. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Management targets in terms of the index (i.e., model free), the total annual catches and absolute biomass levels: Irefbiascv, Crefbiascv, Brefbiascv
Irefbiascv: Log-normal coefficient of variation for sampling persistent bias in relative abundance index at BMSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5
No justification provided.
Crefbiascv: Log-normal coefficient of variation for sampling persistent bias in MSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5
No justification provided.
Brefbiascv: Log-normal coefficient of variation for sampling persistent bias in BMSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5
No justification provided.
Depletion bias and imprecision: Dbiascv, Dobs
Dbiascv: Log-normal coefficient of variation for sampling persistent bias in stock depletion. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5
No justification provided.
Dobs: Log-normal coefficient of variation controlling error in observations of stock depletion among years. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2, 0.4
No justification provided.
Recruitment compensation and trend: hbiascv, Recbiascv
hbiascv: Log-normal coefficient of variation for sampling persistent bias in steepness. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
No justification provided.
Recbiascv: Log-normal coefficient of variation for sampling persistent bias in recent recruitment strength. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1, 0.1
No justification provided.
Obs Plots
Imp Parameters
Output Control Implementation Error: TACFrac, TACSD
TACFrac: Mean fraction of TAC taken. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 0.01, 0.02
No justification provided.
TACSD: Log-normal coefficient of variation in the fraction of Total Allowable Catch (TAC) taken. Uniform distribution lower and upper bounds. Non-negative real numbers.
Specified Value(s): 1, 1
No justification provided.
Effort Control Implementation Error: TAEFrac, TAESD
TAEFrac: Mean fraction of TAE taken. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 0.01, 0.02
No justification provided.
TAESD: Log-normal coefficient of variation in the fraction of Total Allowable Effort (TAE) taken. Uniform distribution lower and upper bounds. Non-negative real numbers.
Specified Value(s): 1, 1
No justification provided.
Size Limit Control Implementation Error: SizeLimFrac, SizeLimSD
SizeLimFrac: The real minimum size that is retained expressed as a fraction of the size. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 1, 1
No justification provided.
SizeLimSD: Log-normal coefficient of variation controlling mismatch between a minimum size limit and the real minimum size retained. Uniform distribution lower and upper bounds. Non-negative real numbers.
Specified Value(s): 0.01, 0.02
No justification provided.
Imp Plots
OM Plots
